PRPF6 p.Ser810=
c.2430C>T · rs149233905 · VCV1061690
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0281%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -3.6 |
| Overall | ||
| CADD | 0.193 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0281%
African / African-American · 21/74,766 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00286%
46/1,609,102 alleles · ultra-rare
exomes 33/1,457,070 · genomes 13/152,032 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0281% | 3,560 |
| South Asian | 0.00554% | 18,065 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,153 |
| Admixed American | 0.00167% | 59,810 |
| European (non-Finnish) | 0.00144% | 69,276 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PRPF6
- Protein
- p.Ser810=
- Coding
- c.2430C>T
- MANE Select
- NM_012469
- dbSNP
- rs149233905
- Type
- single nucleotide variant
- Location
- chr20:64028568 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.07 · 33 PDB
Similar variants
- PRPF6 c.2028+5G>A Uncertain significance ★★ same type
- PRPF6 c.2205+5G>A Uncertain significance ★★ same type
- PRPF6 c.439-19G>A Uncertain significance ★★ same type
- PRPF6 p.Ala246Val Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala380Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala564Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala65Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala675Thr Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prpf6-p-ser810 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown